Group:SMART:2010 Pingry SMART Team Models: Difference between revisions

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'''Return to 2010 SMART Team Page:''' [[2010 Pingry SMART Team]]
<StructureSection load='AdhD_with_three_cofactors_no_H.pdb' size='450' side='right' scene='2010_Pingry_SMART_Team/Adhd_final_default/2' caption=''>
'''Return to 2010 SMART Team Page:''' [[Group:SMART:2010 Pingry SMART Team | 2010 Pingry SMART Team]]
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Sheet color (red): [255,128,128]
Sheet color (red): [255,128,128]


Three residues (ARG, SER, ASN; residue numbers differ by structure) that bind cofactor:
Three residues (ARG-R, SER-S, ASN-N; residue numbers differ by structure) that bind cofactor: display sidechains and color CPK


CPK the sidechain, color backbone (dark blue) [128,128,255]
== AdhD K249G/H255R double mutant ==
 
'''Design description'''
 
(β/α)8 secondary structure features colored blue and red.
 
Two mutated residues have backbone colored blue: K249G and H255R
 
Residues involved in cofactor binding and commonly seen in AKR's have sidechains highlighted: S251, N252, and H255R.
 
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nad/2'>Show NAD</scene>
 
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nadp/1'>Show NADP</scene>
 
<scene name='2010_Pingry_SMART_Team/Adhd_final_default_nmn/1'>Show nicotimanide</scene>
 
<scene name='2010_Pingry_SMART_Team/Adhd_final_default/2'>Return to default</scene>


== AdhD K249G/H255R double mutant and Self-assembly into hydrogels ==
<applet load='AdhD_with_three_cofactors_no_H.pdb' size='400' frame='true' align='right' caption='AdhD K249G/H255R double mutant' scene='2010_Pingry_SMART_Team/Adhd_0/2'/>


'''Design script:'''
'''Design script:'''


Select all
Select all  
 
Backbone off
 
Wireframe off
 
Spacefill off
 
Cartoon off
 
Backbone 300
 
Color white


Backbone off
Select (253-260) or (230-241) or (190-198) or (157-165) or (131-144) or (98-112) or (68-78) or (40-53)


Wireframe off
Color [128,128,192]


Spacefill off
Select (118-122) or (149-153) or (174-177) or (201-205) or (244-249) or (22-25) or (57-61) or (86-91)


Cartoon off
Color [255,128,128]


Backbone 300
Select 249 and (sidechain or alpha)


Color white
Wireframe 250


Select (253-260) or (230-241) or (190-198) or (157-165) or (131-144) or (98-112) or (68-78) or (40-53)
Select 249 and sidechain


Color [128,255,255]
Color cpk


Select (118-122) or (149-153) or (174-177) or (201-205) or (244-249) or (22-25) or (57-61) or (86-91)
Select 249 and alpha


Color [255,128,128]
Color [0,0,255]  


Select 249 and (sidechain or alpha)
Select 255 and (sidechain or alpha)  


Wireframe 250
Wireframe 250  


Select 249 and sidechain
Select 255 and sidechain  


Color cpk
Color cpk  


Select 249 and alpha
Select 255 and alpha  


Color [0,0,255]
Color [0,0,255]  


Select 255 and (sidechain or alpha)
Select (251 or 252) and (sidechain or alpha)


Wireframe 250
Wireframe 250


Select 255 and sidechain
Select (251 or 252) and (sidechain)


Color cpk
Color cpk


Select 255 and alpha
Select 5
 
Color [0,0,128]
 
Select 276


Color [0,0,255]
Color [128,0,0]


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==PDB ID: 1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type)==


<applet load='1a80' size='400' frame='true' align='right' caption='1a80, 2,5-diketo-d-gluconic acid reductase with NADPH (wild-type)' scene='2010_Pingry_SMART_Team/1a80-original/22'/>
==PDB ID: [[1m9h]], Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
<scene name='2010_Pingry_SMART_Team_Models/1m9h_final/3'>Mutant 2,5-diketo-d-gluconic acid reductase with NADH</scene>
 
'''Design description'''
 
(β/α)8 secondary structure features colored blue and red.
 
Four mutated residues have backbone colored orange: F22Y, K232G, R238H, A272G
 
Other residues involved in cofactor binding: S233, V234, W187
 
Amino terminus colored dark blue: [0,0,128]
 
Carboxyl terminus colored cherry: [128,0,0]
 
NADH shown in wireframe
 
 
'''Design script'''


Select all


Backbone off


Wireframe off


{{Clear}}
Spacefill off
 
Select *a
 
Color white
 
Backbone 350
 
Select nad
 
Wireframe 300
 
Color cpk
 
Select (142-154) or (170-181) or (117-130) or (84-98) or (48-63) or (26-39) or (236-246) or (214-225)
 
Color [128,128,192]


==PDB ID: 1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH (mutant)==
Select (18-21) or (43-45) or (71-76) or (102-107) or (133-139) or (159-163) or (183-187) or (228-231)


<applet load='1m9h' size='400' frame='true' align='right' caption='1m9h, Mutant 2,5-diketo-d-gluconic acid reductase with NADH' scene='2010_Pingry_SMART_Team/1m9h_default/1'/>
Color [255,128,128]


Select (22 or 232 or 238 or 272) and (sidechain or alpha)
Select (22 or 232 or 238 or 272) and (sidechain or alpha)
Wireframe 250
 
Wireframe 300
 
Select (22 or 232 or 238 or 272) and sidechain
Select (22 or 232 or 238 or 272) and sidechain
Color cpk
Color cpk
Select (22 or 232 or 238 or 272) and alpha
Select (22 or 232 or 238 or 272) and alpha
Color [255,128,0]
Color [255,128,0]


Select (233 or 234) and (sidechain or alpha)
Select (233 or 234) and (sidechain or alpha)
Wireframe 250
 
Wireframe 300
 
Select (233 or 234) and sidechain
Select (233 or 234) and sidechain
Color CPK
Color CPK


Select 187 and (sidechain or alpha)
Select 187 and (sidechain or alpha)
Wireframe 250
 
Wireframe 300
 
Select 187 and sidechain
Select 187 and sidechain
Color CPK
Color CPK


Display sidechain
Select 2
Color sidechain CPK
 
Color [0,0,128]
 
Select 278
 
Color [128,0,0]


{{Clear}}
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==PDB ID: 1mi3, Xylose reductase with NAD+==
==PDB ID: [[1mi3]], Xylose reductase with NAD+==
<scene name='2010_Pingry_SMART_Team_Models/1mi3_final/7'>Xylose reductase with NAD+</scene>
<applet load='1MI3_chainA.pdb' size='400' frame='true' align='right' caption='1mi3, Xylose reductase with NAD+' scene='2010_Pingry_SMART_Team_Models/1mi3_model/1'/>


Select all


Cartoon off
'''Design description'''
 
(β/α)8 secondary structure features colored blue and red.
 
Three residues involved in NAD+ binding have backbones colored green: E227, N276, R280.
 
Two additional residues involved in NADP+ binding but not NAD+ binding have sidechains displayed but backbone uncolored: K274 or S275.
 
Other residues involved in cofactor binding: S233, V234, W187, Y217
 
Loops that make a conformational change to bind NAD+ or NADP+ colored yellow.
 
Amino terminus colored dark blue: [0,0,128].
 
Carboxyl terminus colored cherry: [128,0,0].
 
NAD+ shown in wireframe.
 
 
'''Design script'''
 
Select all
 
Cartoon off  


Spacefill off
Spacefill off  


Backbone 300
Backbone 350


Color white
Color white  


Select hetero and not water
Select nad


Wireframe 250
Wireframe 250  


Color cpk
Color cpk  


Select 27-41 or 54-68 or 89-104 or 146-160 or 172-183 or 200-210 or 255-266 or 277-286
Select 28-41 or 55-68 or 89-103 or 147-160 or 173-182 or 201-210 or 256-266 or 278-287


Color [128,255,255]  
Color [128,128,192]


Select 20-22 or 45-47 or 77-82 or 108-113 or 163-169 or 189-193 or 213-217 or 270-271  
Select 19-22 or 45-49 or 77-81 or 110-112 or 165-169 or 189-192 or 213-217 or 269-271  


Color [255,128,128]  
Color [255,128,128]


Select 274-280  
Select 274-280  


Color [255,255,0]
Color [255,255,0]  
 
Select 225-229
 
Color [255,255,0]
 
select (227 or 276 or 280) and (sidechain or alpha)
 
wireframe 250


Select 225-229
select (227 or 276 or 280) and (sidechain)


Color [255,128,0]
color cpk


select (275 or 276 or 280) and (sidechain or alpha)
select (227 or 276 or 280) and (alpha)  


wireframe 250
color [255,128,0]


select (275 or 276 or 280) and (sidechain)
select (274 or 275) and (sidechain or alpha)  


color cpk
wireframe 250


select (275 or 276 or 280) and (alpha)
select (274 or 275) and (sidechain)  


color [128,128,255]
color cpk


select (274 or 227) and (sidechain or alpha)
select (217) and (sidechain or alpha)


wireframe 250
wireframe 250


select (274 or 227) and (sidechain)
select 217 and sidechain


color cpk
color cpk
Select 4
Color [0,0,128]
Select 322
Color [128,0,0]


{{Clear}}
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==PDB ID: 1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
==PDB ID: [[1afs]], Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone==
<scene name='2010_Pingry_SMART_Team_Models/1afs_final2/1'>Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone</scene>
'''Model description'''
 


<applet load='1AFS_chainA.pdb' size='400' frame='true' align='right' caption='1afs, Rat liver 3-alpha-hydroxysteroid dihydrodiol dehydrogenase with cofactor and testosterone' scene='2010_Pingry_SMART_Team/1afs_default/7'/>
'''Model script'''


select all


select all
backbone off


backbone off
spacefill off  


spacefill off
cartoon off  


cartoon off
wireframe off  


wireframe off
backbone 350


backbone 300
color white


color white
select tes or nap


select hetero and not water
wireframe 250


wireframe 250
color cpk
 
select sheet
 
select (188-191) or (162-166) or (113-115) or (81-84) or (49-52) or (19-22) or (267-270) or (212-216)


color cpk
color [255,128,128]


select 274-284 or 252-263 or 200-209 or 170-178 or 145-156 or 92-106 or 58-71 or 31-44


color [128, 128, 192]


select sheet
select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain or alpha)


color [255, 128, 128]
wireframe 250


select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain)


color cpk


select 274-284 or 253-263 or 200-209 or 170-177 or 145-156 or 92-106 or 58-70 or 31-43
select (50 or 55 or 84) and (sidechain or alpha)


color [128, 255, 255]
wireframe 250


select (50 or 55 or 84) and (sidechain)


color [128,0,128]


select (54 or 86 or 118 or 120 or 122 or 128 or 129 or 137 or 139 or 227) and (sidechain)
select (28 or 224) and (sidechain or alpha)  


wireframe 250
wireframe 250  


color cpk
select (28 or 224) and (sidechain)


select (50 or 55 or 84) and (sidechain)
color [0,128,0]


wireframe 250
select (276 or 271 or 273 or 216) and (sidechain or alpha)


color [128,0,128]
wireframe 250


select (28 or 224) and (sidechain)
select (276 or 273 or 271 or 216) and (sidechain)


wireframe 250
color cpk


color [0,255,0]
select (24 or 166 or 167 or 190 or 216 or 219 or 221 or 270 or 271 or 272 or 276 or 273) and (alpha)


select (24 or 166 or 167 or 190 or 216 or 219 or 221 or 270  or 271 or 272 or 276) and (sidechain)
color [255,128,0]


wireframe 250
select 116-142 and backbone


color [255,127,0]
color [0,0,255]  


select 116-142 and backbone
select 217-235 and backbone  


color [0,0,255]
color [0,0,255]  


select 217-235 and backbone
Select 1


color [0,0,255]
Color [0,0,128]  


Select 319


Color [128,0,0]




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